WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions, filtered to microbe.
A Gram-negative, aerobic, non-fermenting coccobacillus and a member of the ESKAPE group of priority pathogens (Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, Enterobacter). Acinetobacter baumannii is among the most problematic nosocomial pathogens…
WHO Priority 1: Critical. A Gram-negative, strictly aerobic coccobacillus and one of the most dangerous nosocomial pathogens on the planet. A. baumannii belongs to the ESKAPE group and causes ventilator-associated pneumonia, wound infections, and bloodstream infections …
Aeromonas is a genus of Gram-negative, facultatively anaerobic bacteria found in aquatic environments and, increasingly recognized as an opportunistic gut pathogen. Several species — particularly Aeromonas hydrophila, A. veronii, and A. caviae — are associated with gast…
Alishewanella is a genus of Gram-negative, facultative anaerobic bacteria within the class Gammaproteobacteria. Primarily known as environmental organisms, Alishewanella species have been identified in the microbiome of deep endometriosis — both in vaginal samples and w…
A genus of Gram-positive obligate anaerobes in the family Lachnospiraceae (Clostridium cluster XIVa) that occupy a critical metabolic relay position in gut ecosystem stability: converting lactate to butyrate. Anaerostipes is one of the most consistently depleted genera …
Atopobium is a genus of obligate anaerobic, Gram-positive bacteria in the phylum Actinobacteria. The primary species of clinical relevance is A. vaginae (recently reclassified as Fannyhessea vaginae), which is one of the hallmark organisms of bacterial vaginosis (BV) an…
A Gram-negative obligate anaerobe that exemplifies the commensal-pathobiont spectrum. B. vulgatus is a common component of the healthy gut microbiota, yet is significantly enriched in colorectal cancer and depression, suggesting a context-dependent pathogenic potential.…
Bifidobacteriales is an order of Gram-positive, strictly anaerobic bacteria within the phylum Actinobacteria. The order contains the family Bifidobacteriaceae, which includes the genus Bifidobacterium — among the most widely studied probiotic organisms and a hallmark of…
Bifidobacterium adolescentis is a Gram-positive, obligate anaerobic species within the phylum Actinobacteria and the dominant Bifidobacterium species in the adult human gut. It is a specialist degrader of resistant starch and dietary fiber, producing acetate and lactate…
Bifidobacterium breve is a Gram-positive, obligate anaerobic species within the phylum Actinobacteria, predominantly found in the infant gut and breast milk. It is among the earliest colonizers of the neonatal intestine and plays a key role in human milk oligosaccharide…
Burkholderiales is an order of Gram-negative Betaproteobacteria that includes environmentally versatile genera such as Ralstonia, Burkholderia, and Sutterella. Many members are notable for their metal resistance mechanisms, which enable survival in heavy metal-contamina…
A genus of Gram-positive, strictly anaerobic, butyrate-producing bacteria in the order Clostridiales (phylum Firmicutes). The type species, Butyricicoccus pullicaecorum, was originally isolated from chicken caecal content but has since been identified as a significant m…
A Gram-negative, obligate anaerobic genus within the Bacteroidetes phylum (family Odoribacteraceae). Despite its relatively recent characterization, Butyricimonas has gained significant attention as a member of the protective butyrate-producing consortium that is consis…
Candida tropicalis is an opportunistic fungal pathogen and occasional gut commensal, increasingly recognized as one of the most clinically significant non-albicans Candida (NAC) species. Once considered a distant runner-up to C. albicans, it has emerged as a major drive…
Caulobacter is a genus of Gram-negative obligate aerobic Alphaproteobacteria, with C. crescentus serving as one of the premier model organisms for studying bacterial cell biology. Found primarily in oligotrophic freshwater environments, Caulobacter is not a gut commensa…
Clostridium symbiosum is a Gram-positive, obligately anaerobic bacterium within the Clostridium cluster XIVa — a taxonomic group enriched for short-chain fatty acid (SCFA) producers and specialized bile acid metabolizers. Despite its ambiguous name (suggesting symbiotic…
A genus of Gram-positive, obligate anaerobic bacteria within the Actinobacteria phylum (family Coriobacteriaceae) that has emerged as a consistent pathobiont enriched in cardiometabolic and autoimmune diseases. C. aerofaciens is the most studied species, with establishe…
A Gram-positive, obligate anaerobic genus within the lachnospiraceae family (Firmicutes phylum). Coprococcus is one of the most important butyrate-producing commensals in the human gut and has gained particular attention as the "happiness bug" -- one of very few taxa di…
Debaryomyces is a genus of ascomycetous fungi, with D. hansenii being the most clinically relevant species, that represents a prominent opportunistic pathobiont enriched in inflammatory bowel disease, particularly crohns disease. Unlike many commensal fungi, Debaryomyce…
A Gram-positive, obligate anaerobic genus within the lachnospiraceae family (Firmicutes phylum). Dorea occupies a mixed role in the gut ecosystem -- while it is a core member of the healthy human microbiome, several species are consistently enriched in autoimmune and ne…
Eggerthella is a genus of Gram-positive, strictly anaerobic, non-spore-forming bacteria in the family Eggerthellaceae (phylum Actinobacteria). The most studied species, Eggerthella lenta, was originally classified as Eubacterium lentum before reclassification. It is a n…
A genus of Gram-positive bacteria (primarily E. faecalis and E. faecium) that exemplifies the metal-antibiotic resistance co-selection crisis. Enterococci carry diverse metal tolerance genes for mercury, arsenic, copper, and cadmium on the same mobile genetic elements a…
Enterococcus faecalis is a Gram-positive, facultatively anaerobic coccus that inhabits the gastrointestinal tract, oral cavity, and genitourinary tract of humans. It is a commensal in the healthy gut at low abundance but is one of the most clinically significant opportu…
Escherichia is a genus of Gram-negative, facultatively anaerobic bacteria in the Enterobacteriaceae family. The primary species E. coli is simultaneously the most studied bacterium in biology and one of the most consistently enriched organisms in disease-associated micr…
A Gram-negative bacterium that spans the commensal-pathogen spectrum, with pathogenic variants (UPEC, STEC, EHEC) deploying nickel-dependent enzymes as virulence factors. E. coli is the model organism for nickel transport biology -- the NikABCDE system was first charact…
Firmicutes (recently reclassified as Bacillota) is the dominant bacterial phylum in the Western adult gut, comprising the core community of short-chain fatty acid (SCFA) producers that maintain intestinal barrier integrity, regulate immune function, and influence system…
Flavobacterium is a genus of Gram-negative, aerobic bacteria within the phylum Bacteroidetes. Primarily environmental organisms found in soil and freshwater, Flavobacterium species have been identified in human microbiome studies of the cervical and reproductive tract, …
A Gram-negative, obligate anaerobic bacterium that has emerged as the most consistently CRC-associated microorganism in human gut microbiome studies. F. nucleatum is the primary species of concern, originally a commensal of the oral cavity that translocates to colorecta…
A Gram-negative obligate anaerobe that has emerged as a major pathogen in colorectal cancer (CRC) and inflammatory bowel disease. F. nucleatum is significantly enriched in CRC tissue and tumors compared to healthy mucosa, making it one of the strongest microbe-cancer as…
Gardnerella vaginalis is a Gram-variable, facultatively anaerobic bacterium that is the key organism in bacterial vaginosis (BV), the most common vaginal infection in women of reproductive age. Its sialidase production, biofilm-forming capacity, and associations with he…
Gordonibacter is a genus of Gram-positive, strictly anaerobic gut bacteria within the phylum Actinobacteria. It is recognized as a key participant in polyphenol metabolism, producing bioactive metabolites including equol (from dietary isoflavones) and urolithins (from e…
Lachnospira eligens (Holdeman and Moore 1974) García-López et al. 2020 is the selected current name for NCBITaxon:39485. NCBI Taxonomy lists Eubacterium eligens as its basionym, and LPSN treats the two combinations as homotypic synonyms based on the same type strain, AT…
A genus of Gram-positive, facultatively anaerobic lactic acid bacteria (LAB) that are among the most extensively studied probiotics. In the metallomics context, Lactobacillus species are critical for two reasons: they actively detoxify heavy metals through binding and s…
Lactobacillus plantarum is one of the most versatile probiotic species — found in fermented foods (kimchi, sauerkraut, sourdough), the human gut, and the vaginal microbiome. It has the largest genome among Lactobacillus species (~3.3 Mb), encoding extensive stress toler…
A Gram-negative obligate anaerobe traditionally considered an oral commensal, but increasingly recognized as an opportunistic pathobiont with the ability to translocate from oral biofilms to the gastrointestinal tract and bloodstream. Leptotrichia species are prominentl…
Megasphaera is a genus of obligate anaerobic, Gram-negative bacteria in the family Veillonellaceae (class Negativicutes, phylum Firmicutes). The genus occupies two distinct ecological niches — the vaginal microbiome (where it is a hallmark of bacterial vaginosis) and th…
The only archaeon represented in this wiki -- Methanobrevibacter smithii is the dominant methane-producing microorganism in the human gut, belonging to the domain Archaea rather than Bacteria. As a hydrogenotrophic methanogen, it converts H2 + CO2 into methane (CH4), pl…
A class of bacteria within the phylum Tenericutes defined by the complete absence of a cell wall -- the smallest self-replicating organisms known, with minimal genomes (580 kb-1.4 Mb). While Mollicutes are best known through their pathogenic members (Mycoplasma pneumoni…
Mycoplasma is a genus of wall-less bacteria in the class Mollicutes, characterized by the smallest genomes of any self-replicating organisms (~580–1,350 kb). The lack of a cell wall makes them intrinsically resistant to beta-lactam antibiotics and undetectable by Gram s…
A Gram-negative, obligate anaerobic genus within the Bacteroidetes phylum, closely related to bacteroides fragilis. The best-characterized species, P. distasonis, has emerged as a key anti-inflammatory commensal with significant roles in bile acid metabolism and metabol…
Parvimonas micra is a small (0.5–1.0 µm), Gram-positive, obligately anaerobic coccus originally isolated from the human oral cavity that has emerged as one of the most consistent and universally enriched pathobionts in colorectal cancer across all geographic regions, ag…
A Gram-positive, obligate anaerobic genus that has emerged as one of the most consistently enriched taxa in colorectal cancer. The key pathogenic species P. anaerobius promotes colorectal carcinogenesis through multiple mechanisms including cholesterol biosynthesis indu…
A Gram-negative, obligate anaerobic genus within the phylum Bacteroidota (formerly Bacteroidetes) that was recently reclassified from Bacteroides based on phylogenomic evidence (Garcia-Lopez et al., 2019). The key species -- Phocaeicola vulgatus (formerly Bacteroides vu…
A Gram-negative, obligate anaerobic genus with the keystone pathogen P. gingivalis at its center. Named for its porphyrin (heme) requirement, Porphyromonas is the prototypical periodontal pathogen and one of the most important organisms connecting oral health to systemi…
A Gram-negative obligate anaerobe and keystone pathogen of the oral microbiome that causes chronic periodontitis and is increasingly implicated in systemic diseases including alzheimers disease and cardiovascular disease. P. gingivalis virulence is fundamentally depende…
A Gram-negative, obligate anaerobic genus within the Bacteroidetes phylum that exemplifies context-dependent microbiome effects -- beneficial in some settings, pathogenic in others. P. copri is the dominant species in the human gut and a hallmark of plant-rich, fiber-ri…
A Gram-negative obligate anaerobe that occupies a unique context-dependent niche in the human gut microbiome. P. copri is significantly enriched in rheumatoid arthritis patients and is associated with metabolic syndrome and obesity, yet in other contexts it can function…
A Gram-negative uropathogen whose Ni-dependent urease is the central driver of catheter-associated urinary tract infection (CAUTI) pathogenesis. Urease-mediated urea hydrolysis produces ammonia and alkalinizes urine, triggering precipitation of struvite (magnesium ammon…
An opportunistic Gram-negative pathogen with a unique dual-use siderophore system: its pyoverdine and pyochelin serve not only as iron scavengers but as extracellular chelators of toxic metals including nickel, copper, and cadmium. This makes P. aeruginosa unusually wel…
Ralstonia is a genus of Gram-negative, aerobic bacteria in the class Betaproteobacteria. While Wikipedia focuses on R. solanacearum (a plant pathogen), the WikiBiome-relevant species are R. pickettii and R. metallidurans (now Cupriavidus metallidurans) — organisms with …
A genus of Gram-positive, obligate anaerobic, flagellated bacteria within the lachnospiraceae family that ranks among the most important butyrate producers in the human gut. Key species include R. intestinalis and R. hominis. Roseburia is consistently depleted across in…
Rothia is a genus of Gram-positive, facultatively anaerobic bacteria in the family Micrococcaceae (phylum Actinobacteria). The most commonly identified species in microbiome studies are Rothia dentocariosa and Rothia mucilaginosa, both of which are primary inhabitants o…
A Gram-positive obligate anaerobe that has emerged as a pro-inflammatory pathobiont enriched across multiple disease states including crohns disease, depression, and multiple sclerosis. R. gnavus produces a species-specific inflammatory polysaccharide that activates int…
See also: saccharomyces (genus page) Saccharomyces boulardii is a non-pathogenic yeast strain used as a probiotic across a wide range of gastrointestinal and inflammatory conditions. Taxonomically a strain of S. cerevisiae, it is phenotypically distinct — optimally acti…
Saccharomyces cerevisiae is a unicellular budding fungus (ascomycete) ubiquitous in fermentation, brewing, bread-making, and increasingly used as a pharmaceutical probiotic (Hatoum et al. 2012). The strain S. boulardii (also called S. cerevisiae var. boulardii) is the m…
Salmonella is a genus of Gram-negative, facultatively anaerobic bacteria in the family Enterobacteriaceae. The two species — S. enterica (with 2,500 serovars including Typhimurium and Typhi) and S. bongori — cause a spectrum of disease from self-limiting gastroenteritis…
A Gram-negative enteric pathogen that possesses four distinct hydrogenases of the [NiFe] class -- the most of any well-characterized human pathogen. These hydrogenases are critical for intracellular survival within macrophages, and a triple hydrogenase mutant is 100% av…
A genus of Gram-negative, crescent-shaped, strictly anaerobic bacteria found in both the oral cavity and the gastrointestinal tract. Selenomonas species are characterized by their distinctive morphology -- a curved rod with a tuft of flagella arising from the concave si…
Serratia marcescens is a Gram-negative, facultatively anaerobic member of the Enterobacteriaceae, historically recognized by its distinctive red pigment prodigiosin. Once considered a harmless environmental saprophyte, S. marcescens is now recognized as a significant op…
Sphingobium is a genus of Gram-negative, aerobic bacteria within the family Sphingomonadaceae. Primarily known as environmental organisms capable of degrading aromatic compounds, Sphingobium species have been unexpectedly identified in human microbiome studies of the re…
A genus of Gram-positive, facultative anaerobic cocci that includes some of the most clinically significant human pathogens. Staphylococci are defined by their exceptionally comprehensive metal acquisition arsenal -- arguably the most thoroughly characterized of any bac…
A versatile Gram-positive pathogen with one of the best-characterized nutritional immunity evasion systems known. S. aureus requires nickel, iron, zinc, and manganese for virulence and has evolved dedicated acquisition systems for each, including the novel metallophore …
A genus of Gram-positive facultative anaerobes that occupy niches ranging from benign commensals (dental plaque, skin) to acute pathogens (pharyngitis, impetigo, invasive disease). Streptococci are uniquely manganese-dependent for catalytic scavenging of reactive oxygen…
The primary architect of dental caries -- the most prevalent chronic infectious disease worldwide. S. mutans is a Gram-positive, facultative anaerobe that colonizes tooth surfaces and produces the acid-rich, metal-managed biofilms known as dental plaque. What sets this …
A Gram-positive pathogen (the "pneumococcus") that depends on iron, manganese, and zinc for virulence and has evolved dedicated transport systems for each. Iron is required for viability itself, manganese powers the superoxide dismutase needed to survive the oxidative b…
Streptococcus thermophilus is a Gram-positive, facultative anaerobic coccus that is the primary probiotic species used in commercial yogurt fermentation and thermophilic dairy fermentation worldwide. Distinct from pathogenic Streptococcus species, S. thermophilus produc…
Trichoderma is a genus of filamentous ascomycete fungi ubiquitous in soil and plant root ecosystems. Best known as a biological control agent against plant pathogens, Trichoderma species produce an arsenal of hydrolytic enzymes and antimicrobial compounds. Rarely, they …
A Gram-negative, obligate anaerobic genus within the Firmicutes phylum (class Negativicutes, family Veillonellaceae). The primary species V. parvula is a specialized lactate utilizer that occupies a unique metabolic niche by cross-feeding with lactate-producing bacteria…
The causative agent of plague -- one of the most devastating infectious diseases in human history and a modern bioterrorism concern (Tier 1 Select Agent). Y. pestis depends on nickel for glyoxalase I-mediated metabolic detoxification and produces the archetypal dual-fun…